SIV proviruses seeded later in infection are harbored in short-lived CD4+ T cells

Abstract

The human immunodeficiency virus (HIV) can persist in a latent form as integrated DNA (provirus) in resting CD4⁺ T cells unaffected by antiretroviral therapy. Despite being a major obstacle for eradication efforts, it remains unclear which infected cells survive, persist, and ultimately enter the long-lived reservoir. Here, we determine the genetic divergence and integration times of simian immunodeficiency virus (SIV) envelope sequences collected from infected macaques. We show that the proviral divergence and the phylogenetically estimated integration times display a biphasic decline over time. Investigating the dynamics of the mutational distributions, we show that SIV genomes in short-lived cells are, on average, more diverged, while long-lived cells contain less diverged virus. The change in the mutational distributions over time explains the observed biphasic decline in the divergence of the proviruses. This suggests that long-lived cells harbor viruses deposited earlier in infection, while short-lived cells predominantly harbor more recent viruses.

Keywords: CP: Microbiology; HIV; SIV; antiviral treatment; genetic divergence; latency.

Figure 1.. Biphasic divergence decline

Biphasic divergence decline of non-defective proviral env sequences while on suppressive ART (mean divergence curve shown in red), with an initial rapid decline followed by a second slower decline. Divergence in individual sequences is shown as circles (non-defective proviral env divergence as gray circles and plasma viral env RNA divergence as blue circles). The first slope is shown by blue lines, using non-defective proviral env DNA at the start of ART as a solid line and using plasma viral env RNA at the start of ART as a dashed line. The second slope is shown by a black solid line. Divergence was computed from the consensus sequence of the SIVmac₂₅₁ swarm. Plasma viral RNA could not be collected for macaque T624.

Figure 2.. Integration time

Phylogenetic analyses for macaques (A) T530, (B) T623, (C) T625, and (D) T627, for whom pre-ART sequences were available. The tips in the phylogenetic trees corresponding to samples obtained pre-ART are colored red, while those obtained on-ART are colored blue, with a gradient such that samples obtained later are lighter. The inset plot for each macaque shows the estimated integration time for each proviral non-defective env DNA sequence collected on-ART (circles, colored in the same way as the tips in the phylogenetic tree) and the mean integration time for each such time point (black line) on the left $y$ axis. The right $y$ axis shows the divergence dynamics of the on-ART sequences (dark green line). All times are in terms of weeks since the start of the study.

Figure 3.. Mutational distributions in short- and long-lived cells

Mutational distributions of proviruses in short-lived (orange) and long-lived (gray) populations at the start of ART. Orange and gray curves show the smoothed-out histograms. Solid vertical lines correspond to the mean divergence of short-lived (orange) and long-lived (gray) populations. Vertical green dashed lines show the median divergence of the total population

Figure 4.. Model schematic

Schematic figure of the decay model used in this work. Divergence is computed using Equation 1.

Figure 5.. Experimental and simulated divergence dynamics

Empirically observed mean divergence dynamics (red lines) compared to model simulated divergence. Divergence dynamics using CD4⁺ T cell half-lives estimated by first pooling the data of all 10 macaques and then adjusting for individual variations are shown by blue lines. Divergence dynamics using half-lives learned separately for each individual macaque are shown by green lines. Bold blue/green lines show the means of 10³ simulations. Thin blue/green lines show individual stochastic simulations of divergence obtained by sampling according to experimental times and number of sequences. Turquoise is the result of the thin blue and green lines overlapping. For macaque T523, the blue and green lines overlap exactly, causing only the green lines to be visible. For macaques T624 and T625, green lines are absent, as the data were insufficient to estimate half-lives individually. In T624, the thin blue lines overlap exactly with the thick blue line after ≈20 weeks. The red tick marks on the $x$ axis show the times when experimental samples were obtained